Genome-Wide Identification and Expression Analysis of CAMTA Gene Family Implies PbrCAMTA2 Involved in Fruit Softening in Pear

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Abstract

CAMTA are calcium-modulating binding transcription factors that contribute to plant development. We identified 46 CAMTA genes from eight Rosaceae species and divided them into five subgroups based on a phylogenetic tree. Our analysis indicated that CAMTA is a highly conserved family among Rosaceae species, with a conserved DNA-binding domain (CG-1) and a conserved transcription factor immunoglobulin domain (TIG). Following a recent whole-genome duplication event, the genomes of Chinese white pear, European pear, and apple experienced significant expansion, resulting in the number of CAMTA genes being twice that of the other species. Cis-element identification showed that the distribution of the zein metabolism regulation-responsive element was different in the promoters of Chinese white pear (55.56%) and European pear (11.11%) CAMTA gene families. The gene expression results showed that PbrCAMTA1, 2, 6, 7 was highly expressed in pear fruit. Among them, PbrCAMTA2 may have a key influence on fruit softening, as observed in transient transformation experiments. In conclusion, our results provide crucial insights into the evolution of the CAMTA gene family in pear and other Rosaceae species and identify a candidate PbrCAMTA gene, which is involved in the dynamic development of pear fruits.

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TBtools - an integrative toolkit developed for interactive analyses of big biological data

Chengjie Chen, Hao Chen, Yi Zhang … (2020)

The rapid development of high-throughput sequencing techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for Biologists integrating various biological data-handling tools), a stand-alone software with a user-friendly interface. The toolkit incorporates over 130 functions, which are designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization. A wide variety of graphs can be prepared in TBtools using a new plotting engine ("JIGplot") developed to maximize their interactive ability; this engine allows quick point-and-click modification of almost every graphic feature. TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer. It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.

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The genome of the pear ( Pyrus bretschneideri Rehd.)

Jun Jun Wu, Zhiwen Wang, Zebin Shi … (2013)

The draft genome of the pear ( Pyrus bretschneideri ) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ∼28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ∼5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S -locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT , C3′H , and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.

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The genome of the domesticated apple (Malus × domestica Borkh.).

Riccardo Velasco, Andrey Zharkikh, Jason P Affourtit … (2010)

We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.